What it does

This tool is part of the Splicescope pipeline for prediction of neuronal maturation using splicing profiles. This tool takes either an exon inclusion ratio matrix file or junction bed files from multiple samples as input and outputs a zip file including prediction results, PCA analysis results and a PCA plot based on reference samples and an html file to summarize the prediction.

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Input formats

• Exon splicing matrix file output from Quantas. Please refer to https://zhanglab.c2b2.columbia.edu/index.php/Quantas_Documentation on how to generate this file format.

Example for splicing matrix file:

event_id                                                NAME                    Sample1 Sample2 Sample3
CA-100036521-14294-117618-117680-170683[INC][40/1][DNT] 100036521//Gm16039      1       0.938   1
CA-100036521-117680-144789-144867-170683[INC][3/42][DNT]100036521//Gm16039      0.05    0.014   0
etc.

• Junction BED file from mapping software such as TopHat. Please note that these two input formats can not be specified at the same time. Sample label must be specified if using BED file as input. Set labels to the same if you want to merge biological or technical replicates.

Example for junction BED file:

chr1    3207264 3213485 JUNC00000001    1       -       3207264 3213485 255,0,0 2       53,47   0,6174
chr1    3216873 3421784 JUNC00000002    5       -       3216873 3421784 255,0,0 2       95,83   0,204828
etc.

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Output formats

The output file for download would be a zip file including:

• res_pre.txt which includes 10 columns representing the predicted maturation stage and corresponding prediction confidence score using both whole sets of developmentally regulated exons and RBP-Specific targets as reference.

Example:

        Maturation      ConfidenceScore PtbpMaturation  PtbpConfidenceScore     RbfoxMaturation RbfoxConfidenceScore    MbnlMaturation  MbnlConfidenceScore     NovaMaturation  NovaConfidenceScore
Sample1 6               0.119           2               0.149                   6               0.387                   6               0.534                   1               0.323
Sample2 2               0.080           2               0.142                   6               0.361                   6               0.483                   1               0.293
etc.

• res_pca.txt which includes the PC1 and PC2 value used for both user-defined samples and reference cortex samples in the plot.

Example:

        PC1     PC2
Sample1 -1.350  2.817
Sample2 -1.907  3.265
etc.

• dataPCA.pdf which is the PCA plot for use-defined samples based on reference samples .
• index.html which summarizes the prediction results and PCA plot.